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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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ciftify_subject_fmri error #45

Closed bamal closed 6 years ago

bamal commented 6 years ago

I tried to convert Nifti a 4D volume to surface and I got this error: 

ciftify_subject_fmri MYBASEDIR/fmri_s0025447_session3_rest.nii.gz 0025447 out
Subject HCPfolder does not exit

Any insights related to this please ?

edickie commented 6 years ago

Hey Amal,

Are you working from the current master or the latest release? I would recommend the latest release...the master is in a little flux in prep for a new release next week.

Sorry, I should have warned about that before, Erin

On Wed, Mar 28, 2018 at 6:37 PM, Amal notifications@github.com wrote:

Trying to convert Nifti a 4D volume to surface I got this error:

ciftify_subject_fmri fmri_s0025447_session3_rest.nii.gz 0025447 out Traceback (most recent call last): File "/home/boukhdha/anaconda3/bin/ciftify_subject_fmri", line 11, in load_entry_point('ciftify==1.0.1', 'console_scripts', 'ciftify_subject_fmri')() File "/home/boukhdha/anaconda3/lib/python3.6/site-packages/ciftify/bin/ciftify_subject_fmri.py", line 625, in main if not os.path.exists(os.path.join(HCPData,Subject,'MNINonLinear')): File "/home/boukhdha/anaconda3/lib/python3.6/posixpath.py", line 78, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

Any insights related to this please ?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/edickie/ciftify/issues/45, or mute the thread https://github.com/notifications/unsubscribe-auth/AMl59kHWw3VfdC6XjL5nQHDKbLrhxXOLks5tjBCUgaJpZM4S_eV4 .

edickie commented 6 years ago

Also, did you run ciftify_recon_all to generate the subject surface info before running this step?

Thanks, Erin

On Wed, Mar 28, 2018 at 9:12 PM, Erin W. E. Dickie erin.w.dickie@gmail.com wrote:

Hey Amal,

Are you working from the current master or the latest release? I would recommend the latest release...the master is in a little flux in prep for a new release next week.

Sorry, I should have warned about that before, Erin

On Wed, Mar 28, 2018 at 6:37 PM, Amal notifications@github.com wrote:

Trying to convert Nifti a 4D volume to surface I got this error:

ciftify_subject_fmri fmri_s0025447_session3_rest.nii.gz 0025447 out Traceback (most recent call last): File "/home/boukhdha/anaconda3/bin/ciftify_subject_fmri", line 11, in load_entry_point('ciftify==1.0.1', 'console_scripts', 'ciftify_subject_fmri')() File "/home/boukhdha/anaconda3/lib/python3.6/site-packages/ciftify/bin/ciftify_subject_fmri.py", line 625, in main if not os.path.exists(os.path.join(HCPData,Subject,'MNINonLinear')): File "/home/boukhdha/anaconda3/lib/python3.6/posixpath.py", line 78, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

Any insights related to this please ?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/edickie/ciftify/issues/45, or mute the thread https://github.com/notifications/unsubscribe-auth/AMl59kHWw3VfdC6XjL5nQHDKbLrhxXOLks5tjBCUgaJpZM4S_eV4 .